Contacts of the helix formed by residues 1423 - 1431 (chain M) in PDB entry 3HOU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1423 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859M SER* 3.8 17.5 - - - -
1398M MET* 4.1 8.1 - - - -
1422M ARG* 1.3 80.3 - - - +
1424M VAL* 1.3 68.2 + - - +
1425M SER 3.1 2.5 - - - -
1426M GLU* 3.2 27.3 + - - +
1427M ASN* 2.9 18.6 + - - -
1435M PRO* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1424 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846M GLU* 4.0 15.9 - - + +
847M ASP* 3.7 33.7 - - + +
1063M MET* 4.7 2.5 - - + -
1398M MET* 4.0 2.0 - - - +
1422M ARG 3.8 1.4 + - - -
1423M GLY* 1.3 72.0 - - - +
1425M SER* 1.3 65.4 + - - +
1427M ASN* 3.2 4.7 + - - +
1428M VAL* 3.0 29.3 + - + +
1434M ALA* 4.2 14.3 - - + +
1435M PRO* 5.7 0.9 - - - -
1436M ILE* 4.1 28.3 - - + -
1135N ARG* 5.5 0.2 - - - +
1139N ILE* 3.5 35.9 - - + -
1147N LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1425 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341M MET* 3.0 26.8 - - - +
843M LYS* 3.3 1.2 + - - -
846M GLU* 2.3 35.3 + - - -
1397M LEU 5.1 0.4 - - - -
1398M MET* 3.6 29.5 - - - +
1401M SER* 4.4 2.0 - - - -
1423M GLY 3.1 0.2 - - - -
1424M VAL* 1.3 81.4 - - - +
1426M GLU* 1.3 63.0 + - - +
1428M VAL* 3.1 6.0 + - - +
1429M ILE* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1426 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859M SER* 5.3 0.3 + - - -
1394M THR* 5.0 0.3 - - - +
1395M GLY* 3.9 6.8 + - - -
1397M LEU* 3.1 26.1 - - + +
1398M MET* 3.2 27.4 + - - +
1419M ASP* 2.7 34.1 - - - +
1421M CYS* 3.5 27.8 - - + -
1422M ARG 4.7 0.2 + - - -
1423M GLY* 3.2 35.1 + - - +
1425M SER* 1.3 74.6 - - - +
1427M ASN* 1.3 56.4 + - - +
1429M ILE* 3.3 9.1 + - - +
1430M LEU* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1427 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421M CYS* 3.3 25.3 + - - +
1422M ARG 4.3 0.2 - - - -
1423M GLY 2.9 23.6 + - - -
1424M VAL 3.2 6.0 + - - +
1425M SER 3.1 0.2 - - - -
1426M GLU* 1.3 75.3 - - - +
1428M VAL* 1.3 58.3 + - - +
1430M LEU* 2.7 6.7 + - - +
1431M GLY 2.6 32.7 + - - -
1432M GLN* 3.2 42.9 + - - +
1433M MET 3.9 5.5 - - - +
1434M ALA* 3.9 15.9 - - + -
1435M PRO* 3.7 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1428 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340M LEU* 3.6 18.6 - - - +
341M MET* 4.2 8.7 - - - -
343M LYS* 5.3 1.4 + - - -
1424M VAL* 3.0 29.0 + - + +
1425M SER* 3.1 10.5 + - - +
1427M ASN* 1.3 76.3 - - + +
1429M ILE* 1.3 60.3 + - - +
1431M GLY* 3.4 10.3 + - - -
1432M GLN 5.1 1.6 - - - -
1434M ALA* 5.3 2.7 - - + +
1135N ARG* 4.1 29.4 - - + +
1147N LEU* 4.3 15.9 - - + -
1151N LEU* 3.5 31.5 - - + +
1197N PRO* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1429 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336M ILE* 4.3 18.8 - - + -
340M LEU* 4.0 28.2 - - + +
341M MET* 3.9 21.5 - - + -
1397M LEU* 3.9 51.4 - - + +
1401M SER* 5.2 0.4 - - - -
1425M SER 2.9 16.8 + - - +
1426M GLU* 3.4 9.4 - - - +
1428M VAL* 1.3 77.7 - - - +
1430M LEU* 1.3 61.8 + - + +
1431M GLY 3.3 0.2 - - - -
1197N PRO* 3.2 20.4 - - - +
1200N ALA* 3.5 10.7 - - + +
1203N LEU* 4.6 6.7 - - + -
1204N PHE* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1430 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M VAL* 3.7 41.1 - - + -
17M VAL* 4.6 4.5 - - + -
1397M LEU* 5.3 3.6 - - + -
1421M CYS* 3.8 19.3 - - + -
1426M GLU* 2.9 18.9 + - + +
1427M ASN* 2.7 9.0 + - - +
1429M ILE* 1.3 79.2 - - + +
1431M GLY* 1.3 64.4 + - - +
1432M GLN* 3.6 28.1 + - - +
1195N HIS 3.5 4.9 - - - +
1196N ILE* 3.5 27.5 - - + +
1197N PRO* 3.3 12.7 - - - +
1204N PHE* 4.2 24.9 - - + -
1216N LEU* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1431 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427M ASN 2.6 12.4 + - - -
1428M VAL* 3.4 7.7 + - - -
1429M ILE 3.3 3.2 - - - -
1430M LEU* 1.3 75.9 - - - +
1432M GLN* 1.3 58.1 + - - +
1148N LYS* 3.6 25.6 - - - +
1151N LEU* 5.6 4.0 - - - -
1152N MET* 3.7 24.7 - - - +
1195N HIS 4.3 1.2 - - - +
1197N PRO* 3.6 13.4 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il